TB-Profiler result

Run: ERR2229394
Summary

Run ID: ERR2229394

Sample name:

Date: 31-03-2023 17:09:38

Number of reads: 702372

Percentage reads mapped: 98.94

Strain: lineage4.8

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
pncA 2288823 p.Arg140His missense_variant 0.12 pyrazinamide
ethA 4326250 p.Tyr408* stop_gained 0.33 ethionamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6335 p.Gln366* stop_gained 0.17
gyrB 6663 p.Phe475Ser missense_variant 0.13
gyrA 7314 p.Thr5Ser missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8072 c.771T>C synonymous_variant 0.22
gyrA 8612 p.Asp437Glu missense_variant 0.13
fgd1 490646 c.-137G>T upstream_gene_variant 0.13
mshA 575780 p.Pro145Ser missense_variant 0.18
mshA 575942 p.Arg199Cys missense_variant 0.18
mshA 576584 c.1237C>A synonymous_variant 0.4
ccsA 620586 c.696C>A synonymous_variant 0.33
ccsA 620610 p.Phe240Leu missense_variant 0.33
ccsA 620853 c.963G>T synonymous_variant 0.22
rpoB 759817 p.Ser4Tyr missense_variant 0.2
rpoB 762602 p.Trp932Cys missense_variant 0.2
rpoC 762842 c.-528G>T upstream_gene_variant 0.14
rpoB 762948 p.Gln1048* stop_gained 0.12
rpoC 763419 p.Ala17Glu missense_variant 0.2
rpoC 763553 p.Cys62Arg missense_variant 0.13
rpoC 764065 c.696G>A synonymous_variant 0.33
rpoC 766592 p.Val1075Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775709 c.2772C>T synonymous_variant 0.14
mmpL5 775736 c.2745C>G synonymous_variant 0.13
mmpL5 775741 c.2740C>T synonymous_variant 0.14
mmpL5 775747 p.Met912Leu missense_variant 0.14
mmpL5 775748 c.2733T>C synonymous_variant 0.14
mmpL5 776003 c.2478C>T synonymous_variant 0.25
mmpL5 777626 p.Tyr285* stop_gained 0.15
mmpS5 778806 p.Ser34Pro missense_variant 0.17
mmpL5 778972 c.-492G>A upstream_gene_variant 0.13
mmpR5 779248 p.Gly87Arg missense_variant 0.29
mmpR5 779320 p.Met111Leu missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801411 c.603C>A synonymous_variant 0.33
fbiC 1303107 c.177C>T synonymous_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304815 p.His629Tyr missense_variant 0.15
Rv1258c 1406242 p.Ala367Ser missense_variant 0.18
embR 1416325 c.1023C>A synonymous_variant 0.12
embR 1417441 c.-94T>C upstream_gene_variant 0.2
atpE 1461065 c.21C>G synonymous_variant 0.13
atpE 1461290 c.246A>T stop_lost&splice_region_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472812 n.967A>G non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474391 n.737delA non_coding_transcript_exon_variant 0.17
rrl 1475001 n.1344A>G non_coding_transcript_exon_variant 0.67
rrl 1475094 n.1437C>G non_coding_transcript_exon_variant 0.25
rrl 1475355 n.1698C>A non_coding_transcript_exon_variant 0.22
rrl 1475359 n.1702G>A non_coding_transcript_exon_variant 0.22
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.25
rrl 1475955 n.2298A>G non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
fabG1 1673762 c.324delC frameshift_variant 0.18
inhA 1674413 p.Leu71Pro missense_variant 0.5
inhA 1674801 c.600T>C synonymous_variant 0.25
rpsA 1833384 c.-158C>A upstream_gene_variant 0.15
rpsA 1833653 p.Ile38Val missense_variant 0.17
rpsA 1834773 p.Arg411His missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918363 p.Glu142* stop_gained 0.15
ndh 2101973 p.Ala357Glu missense_variant 0.18
ndh 2102962 c.81A>G synonymous_variant 0.15
katG 2154721 p.Ala464Glu missense_variant 0.17
katG 2155027 p.Gly362Val missense_variant 0.29
katG 2156534 c.-423G>A upstream_gene_variant 0.12
PPE35 2167814 c.2799C>T synonymous_variant 0.29
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.23
PPE35 2169272 c.1341C>G synonymous_variant 0.25
PPE35 2169278 c.1335T>C synonymous_variant 0.3
PPE35 2169281 c.1332T>G synonymous_variant 0.27
PPE35 2169287 c.1326T>C synonymous_variant 0.33
PPE35 2169293 c.1320T>C synonymous_variant 0.3
PPE35 2169302 p.Met437Phe missense_variant 0.18
PPE35 2169308 c.1305C>T synonymous_variant 0.31
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.63
PPE35 2170238 c.375T>G synonymous_variant 0.14
PPE35 2170564 p.Ala17Pro missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289633 c.-392G>T upstream_gene_variant 0.14
kasA 2518316 p.Val68Leu missense_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.29
kasA 2519143 c.1029G>C synonymous_variant 0.29
kasA 2519153 p.Ile347Val missense_variant 0.2
kasA 2519189 p.Val359Leu missense_variant 0.14
eis 2714344 p.Ala330Val missense_variant 0.25
eis 2714494 p.Thr280Asn missense_variant 0.2
eis 2714567 p.Leu256Met missense_variant 0.22
pepQ 2859430 p.Leu330Ser missense_variant 0.18
ribD 2986794 c.-45G>C upstream_gene_variant 0.12
ribD 2987338 p.Gly167Val missense_variant 0.17
Rv2752c 3064758 c.1434G>T synonymous_variant 0.22
Rv2752c 3066112 p.Ile27Thr missense_variant 0.14
Rv2752c 3066121 p.Ile24Thr missense_variant 0.12
ald 3087494 c.675C>A synonymous_variant 0.22
whiB7 3568869 c.-190C>T upstream_gene_variant 0.18
alr 3840420 p.Arg334Pro missense_variant 0.22
rpoA 3878373 c.135G>T synonymous_variant 0.12
rpoA 3878389 p.Arg40His missense_variant 0.18
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
clpC1 4038244 p.Thr821Ala missense_variant 0.29
clpC1 4038711 p.Thr665Lys missense_variant 0.14
clpC1 4038773 p.Asp644Glu missense_variant 0.13
clpC1 4038776 p.Glu643Asp missense_variant 0.13
clpC1 4039508 c.1197G>C synonymous_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.12
clpC1 4040605 p.Leu34Val missense_variant 0.21
panD 4044087 c.195C>T synonymous_variant 0.2
embC 4240253 p.Val131Leu missense_variant 0.17
embC 4240801 c.939C>T synonymous_variant 0.13
embC 4241526 p.Gly555Asp missense_variant 0.33
embC 4241923 c.2061G>T synonymous_variant 0.17
embC 4241952 p.Arg697Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244864 c.1632G>A synonymous_variant 0.22
embA 4245255 p.Glu675* stop_gained 0.33
embA 4245811 p.Pro860Gln missense_variant 0.2
embA 4245919 p.Trp896Leu missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.42
embB 4246548 p.Pro12Gln missense_variant 0.45
embB 4246555 c.42G>C synonymous_variant 0.62
embB 4246556 p.Ala15Pro missense_variant 0.62
embB 4246567 c.54_55insT frameshift_variant 0.5
embB 4248228 p.Trp572Leu missense_variant 0.17
embB 4248770 p.Val753Leu missense_variant 0.2
aftB 4267850 p.Gln329His missense_variant 0.22
aftB 4268562 p.Leu92Gln missense_variant 0.17
ethA 4326890 p.Ala195Val missense_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.18
ethR 4326964 c.-585G>A upstream_gene_variant 0.18
ethR 4326970 c.-579G>T upstream_gene_variant 0.2
ethA 4327263 p.Gly71Arg missense_variant 0.15
ethA 4327995 c.-522C>A upstream_gene_variant 0.29
ethA 4328306 c.-833C>G upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0